LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -56.954297 0.0000000) to (28.477148 56.954297 3.6461252) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1352235 5.1352235 3.6461252 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.954297 0.0000000) to (28.477148 56.954297 3.6461252) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1352235 5.1352235 3.6461252 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.954297 0.0000000) to (28.477148 56.954297 3.6461252) create_atoms CPU = 0.001 seconds 490 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 27 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_331285495617_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.428 | 5.428 | 5.428 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3610.9995 0 -3610.9995 42808.053 93 0 -3808.3442 0 -3808.3442 5985.4397 Loop time of 2.45162 on 1 procs for 93 steps with 978 atoms 84.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3610.99948953632 -3808.34092999914 -3808.34422152662 Force two-norm initial, final = 233.01730 0.25524169 Force max component initial, final = 44.328783 0.057933867 Final line search alpha, max atom move = 1.0000000 0.057933867 Iterations, force evaluations = 93 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.354 | 2.354 | 2.354 | 0.0 | 96.02 Neigh | 0.048564 | 0.048564 | 0.048564 | 0.0 | 1.98 Comm | 0.035317 | 0.035317 | 0.035317 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01372 | | | 0.56 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900.00 ave 9900 max 9900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 218000.0 ave 218000 max 218000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218000 Ave neighs/atom = 222.90389 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.435 | 5.435 | 5.435 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -3808.3442 0 -3808.3442 5985.4397 11827.272 99 0 -3808.5491 0 -3808.5491 -9.9542449 11869.542 Loop time of 0.0688164 on 1 procs for 6 steps with 978 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3808.34422152661 -3808.54908659198 -3808.54914359428 Force two-norm initial, final = 98.699077 0.44447935 Force max component initial, final = 77.158445 0.26873298 Final line search alpha, max atom move = 0.00072340558 0.00019440294 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065317 | 0.065317 | 0.065317 | 0.0 | 94.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071209 | 0.00071209 | 0.00071209 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002788 | | | 4.05 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9906.00 ave 9906 max 9906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 218168.0 ave 218168 max 218168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218168 Ave neighs/atom = 223.07566 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.573 | 5.573 | 5.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3808.5491 0 -3808.5491 -9.9542449 Loop time of 1.879e-06 on 1 procs for 0 steps with 978 atoms 159.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.879e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9906.00 ave 9906 max 9906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 217856.0 ave 217856 max 217856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217856 Ave neighs/atom = 222.75665 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.573 | 5.573 | 5.573 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3808.5491 -3808.5491 28.408184 114.09333 3.6621002 -9.9542449 -9.9542449 -14.627728 -36.332991 21.097984 2.2998492 152.64343 Loop time of 1.807e-06 on 1 procs for 0 steps with 978 atoms 166.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.807e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9906.00 ave 9906 max 9906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108928.0 ave 108928 max 108928 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 217856.0 ave 217856 max 217856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217856 Ave neighs/atom = 222.75665 Neighbor list builds = 0 Dangerous builds = 0 978 -3808.54914359428 eV 2.29984922053299 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02